Fig. 2: Dynamicity and stage specificity of the developmental proteome of B. mori.

a Scatter plot of the average protein intensities (mean log₂ LFQ intensity of all timepoints) in relation to their dynamicity across development (Gini ratio). A filter of 0.1 (dashed line) for the dynamicity score divides the proteome into proteins with stable and dynamic expression. In the lower part, proteins with stable expression are shown (n = 763), while the upper part contains proteins with dynamic expression (n = 1549). b Temporal expression profiles (mean log₂ LFQ intensities, n = 5 biological replicates, LOD = limit of detection) of two highly stably (Gapdh2 and Hsp60A) and two highly dynamically expressed proteins (CCN and P25) highlighted in orange in (a). Box plots display the expression distribution of the replicates; the horizontal line represents the median and the upper and lower edges of the box depict the interquartile range (IQR). c Heatmap of normalized protein expression (z-score of mean LFQ intensity, n = 5 biological replicates) of 2347 proteins (proteins within the upper 90th percentile of protein-specific variability, measured by interquartile range (IQR) across timepoints, quantified in >= 3 replicates) corresponding to stage-specific clusters (egg = 229 proteins, larva = 1309 proteins, pupa = 449 proteins and adult = 360 proteins). d Protein expression profiles of individual stage-specific clusters generated by unsupervised SOM clustering, plotted as the cluster-wise median z-score normalized mean LFQ intensities (n = 5 biological replicates, same data as in (c)). Box plots show the expression distribution of proteins cluster-wise; the black dot represents the median and box edges represent the IQR. e Gene Ontology (GO) term and Pfam domain enrichment for the proteins associated with the stage-specific clusters (Fisher’s exact test, FDR < 0.05). Each circle represents a GO term or Pfam domain, with the color corresponding to the −log₁₀(FDR) and the size representing the number of proteins associated with the respective category. The top five most significantly enriched terms per stage are depicted (all stage-specific terms in Supplementary Data S2 and cluster-specific in Supplementary Data S3).